79 lines
2.7 KiB
Perl
79 lines
2.7 KiB
Perl
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#!/usr/bin/perl
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#use strict;
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#use warnings;
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die "usage:perl $0 outputDir tumor" unless @ARGV==2;
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my ($outputDir,$tumor)=@ARGV;
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my @hhr=("ATM","BARD1","BRCA1","BRCA2","BRIP1","CDK12","CHEK1","CHEK2","FANCL","PALB2","PPP2R2A","RAD51B","RAD51C","RAD51D","RAD54L","ARID1A","ATR","ATRX",
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"BAP1","BLM","FANCA","FANCC","FANCD2","FANCE","FANCF","FANCG","FANCI","MDC1","MRE11","NBN","PTEN","RAD50","RAD51","XRCC2");
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open OUT,">$outputDir/HRR/${tumor}_hrr.txt";
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open IN1, "$outputDir/mutation/${tumor}.snp.indel.Germline.anno.hg19_multianno_filtered.txt";
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open HRRPRE, ">$outputDir/HRR/${tumor}.hrr.pre.txt";
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my $head=<IN1>;
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my (@content,@hrrpre);
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while(<IN1>){
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chomp;
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my @line=split("\t");
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next unless grep{$line[7] eq $_}@hhr;
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push @hrrpre,$_;
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next if $line[0]!~/1|2|3/;
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my $sig=($line[0]=='1')?'致病突变':($line[0]=='2')?'疑似致病突变':'意义未明突变';
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shift @line;
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if($line[9] ne '.'){
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my $hgvs=$line[9];
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$hgvs=~/:(NM_\d+):exon\d+:(c\.\S+):(p\.\S+)$/;
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my $gene=$line[6];
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my $tr=$1;
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my $codon=$2;
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my $protein=$3;
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my $freq=(split(":",$line[-1]))[-2];
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my $muttype=($line[8]=~/nonsynonymous SNV/)?'错义突变':($line[8]=~/^frameshift/)?'移码突变':($line[8]=~/^nonframeshift/)?'非移码突变':($line[8]=~/stopgain/)?'提前终止':'未知';
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push @content,join("\t",($gene,$tr,$codon,$protein,$freq,$muttype,$sig));
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}
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}
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open IN2, "$outputDir/mutation/${tumor}.snp.indel.Somatic.annoall.hg19_multianno_filtered.txt";
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<IN2>;
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while(<IN2>){
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chomp;
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my @line=split("\t");
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next if $line[0] ne '1';
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next unless grep{$line[7] eq $_}@hhr;
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my $sig;
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if($line[17]=~/Affects|association|Conflicting|sensitivity|drug|other|risk|protective|Uncertain|not_provided|\./i){
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if($line[17]=~/Likely_pathogenic|drug/i){
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$sig="疑似致病突变";
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}elsif($line[17]=~/pathogenic/i and $line[17]!~/Conflicting/i){
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$sig="致病突变";
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}else{
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$sig="意义未明突变";
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}
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}
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next unless $sig;
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shift @line;
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if($line[9] ne '.'){
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my $hgvs=$line[9];
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$hgvs=~/:(NM_\d+):exon\d+:(c\.\S+):(p\.\S+)$/;
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my $gene=$line[6];
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my $tr=$1;
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my $codon=$2;
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my $protein=$3;
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my $freq=(split(":",$line[-2]))[-2];
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my $FREQ=$freq=~s/%//r;
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next if $FREQ<3;
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my $muttype=($line[8]=~/nonsynonymous SNV/)?'错义突变':($line[8]=~/^frameshift/)?'移码突变':($line[8]=~/^nonframeshift/)?'非移码突变':($line[8]=~/stopgain/)?'提前终止':'未知';
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push @content,join("\t",($gene,$tr,$codon,$protein,$freq,$muttype,$sig));
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}
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}
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if (@content){
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print OUT "gene\ttranscript\tc_change\tp_change\tfreq\tmuttype\tsig\n";
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print OUT join("\n",@content);
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}
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if (@hrrpre){
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print HRRPRE $head;
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print HRRPRE join("\n",@hrrpre)."\n";
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}
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